Dear list, 

I´ve already analysed microarray data from Hugene11 st with oligo package. However I would like to use xps package as well because I want to compare results from Hugene 1.0 and Hugene 1.1 and I think xps package is the right one. 
I have created the root scheme following the script proposed in the package: 

scheme.hugene11stv1.na32 <- import.exon.scheme("hugene11stv1", filedir = file.path(scmdir, "na32"), 
+ file.path(libdir, "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.clf"), 
+ file.path(libdir, "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.pgf"), 
+ file.path(anndir, "Version08Oct", "HuGene-1_1-st-v1.na32.hg19.probeset.csv"), 
+ file.path(anndir, "Version08Oct", "HuGene-1_1-st-v1.na32.hg19.transcript.csv")) 
Creating new file </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/schemes/na32/hugene11stv1.root>... 
Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/libraryfiles/HuGene-1_1-st-v1_strip_libraryfile/HuGene-1_1-st-v1.r4.clf> as <HuGene-1_1-st-v1.cxy>... 
<803480> records imported...Finished 
Warning: Number of entries <803480> is not equal to <1178100>. 
New dataset <HuGene-1_1-st-v1> is added to Content... 
Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/Annotation/Version08Oct/HuGene-1_1-st-v1.na32.hg19.probeset.csv> as <HuGene-1_1-st-v1.anp>... 
Number of probesets is <257430>. 
<33297> records read...Finished 
<32919> records imported...Finished 
shed 
> # HuGene-1_0-st-v1.r4: used as exon array 
> scheme.hugene10stv1.na32 <- import.exon.scheme("hugene10stv1", filedir = file.path(scmdir, "na32"), 
+ file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", "HuGene-1_0-st-v1.r4.clf"), 
+ file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", "HuGene-1_0-st-v1.r4.pgf"), 
+ file.path(anndir, "Version11Jul", "HuGene-1_0-st-v1.na32.hg19.probeset.csv"), 
+ file.path(anndir, "Version11Jul", "HuGene-1_0-st-v1.na32.hg19.transcript.csv")) 
Creating new file </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/schemes/na32/hugene10stv1.root>... 
Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/libraryfiles/HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene-1_0-st-v1.r4.clf> as <HuGene-1_0-st-v1.cxy>... 
<1102500> records imported...Finished 
New dataset <HuGene-1_0-st-v1> is added to Content... 
Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis xps/Annotation/Version11Jul/HuGene-1_0-st-v1.na32.hg19.probeset.csv> as <HuGene-1_0-st-v1.anp>... 
Number of probesets is <257430>. 
<33297> records read...Finished 
<32919> records imported...Finished 
shed 

After creating both root schemes (for Hugene 1.0 and 1.1 st) I moved them to a schemes directory in xps package 

However, when I try to import the root schemes I obtained the following error: 
> scheme.hugene11stv1 <- root.scheme(file.path(.path.package("xps"), "schemes", "hugene11stv1.root")) 
Error en validROOTFile(rootfile, "none") : 
‘rootfile’ of class ‘none’ is missing or not a ROOT file *.root 
> scheme.hugene10stv1 <- root.scheme(file.path(.path.package("xps"), "schemes", "hugene10stv1.root")) 
Error en validROOTFile(rootfile, "none") : 
‘rootfile’ of class ‘none’ is missing or not a ROOT file *.root 


Any ideas ? 

Juan 

My sessionInfo is the following: 
R version 2.15.1 (2012-06-22) 
Platform: i386-apple-darwin9.8.0/i386 (32-bit) 

locale: 
[1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 

attached base packages: 
[1] stats graphics grDevices utils datasets methods base 

other attached packages: 
[1] xps_1.16.0 

loaded via a namespace (and not attached): 
[1] tools_2.15.1 




--------------------------------------------------------------- 
Juan Fernandez Tajes, ph. D 
Grupo XENOMAR 
Departamento de Biología Celular y Molecular 
Facultad de Ciencias-Universidade da Coruña 
Tlf. +34 981 167000 ext 2030 
e-mail: jfernandezt@udc.es 
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